San Clemente is the fourth largest of the Channel Islands at 56 square miles in size. Its highest peak is Mount Thirst at 1,956 feet, and the island is primarily marine terraces cut with canyons running down to the shoreline. Like many of the other Channel Islands, San Clemente is composed of volcanic rock formed in the Miocene era, and has sedimentary rock moved up by seismic forces from the ocean floor, which is imbedded with fossils of prehistoric animal and plant life.

The marine terraces on the western side of the island create a gradual incline from the shoreline to the higher inland terraces. As compared to the eastern side with its rocky formidable cliffs, the western side has been more easily inhabited since prehistoric times.

The deep sea canyons off San Clemente are now home to technology research projects for undersea exploration and development, sponsored by the U.S. Navy.

As with its neighbors to the north, San Clemente has a caliche forest, which is an other worldly appearing mineral formation that has adhered to the lifeless remains of low lying vegetation. The caliche formation are made of rhizoconcretions that form eerie, abstract landscapes of bizarre form. The materials that work together to form a caliche forest are calcium carbonate, sand, gravel, silt and clay.